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A PSSM is a Position Specific Scoring Matrix. A profile is one type of PSSM. PSSMs enable the scoring of multiple alignments with sequences, structures etc. There are a number of ways to convert a multiple alignment, such as a block, into a PSSM. The conversion can use the multiple alignment sequence weights, the expected number of amino acids and the frequencies of unobserved amino acids (pseudocounts).

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